scholarly journals Virulence gene, antimicrobial resistance and phylogenetic characterization of Vibrio parahaemolyticus in migratory birds, Guangdong

2020 ◽  
Author(s):  
Lin zheng ◽  
Ping Chen ◽  
Jun Xue Guo ◽  
Ling Wei Zhu ◽  
Yao Jia Guan ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Resistance Genes ◽  
Vibrio Parahaemolyticus ◽  
Migratory Birds ◽  
Virulence Gene ◽  
Migratory Bird ◽  
Phylogenetic Characterization ◽  
Contaminated Food ◽  
Intestinal Pathogen ◽  
Drug Resistant Strains

Abstract Background Vibrio parahaemolyticus is an intestinal pathogen that is transmitted by contaminated aquatic products.Migratory birds ate foods infected with Vibrio parahaemolyticus, excreting feces on other foods. Other organisms ate contaminated food again, leading to the spread of strains. It were reported previously that Vibrio parahaemolyticus was sensitive to most antibiotics except penicillin such as ampicillin and amoxicillin. However, due to the frequent used of antibiotics in recent years, Vibrio parahaemolyticus developed resistance to antibiotics. The recommended antibiotics for Vibrio parahaemolyticus treatment were tetracycline, β-lactam, quinolone and sulfonamide. In the storage migratory bird, Vibrio parahaemolyticus could complete the accumulation of drug resistance, resulting in the generation of drug resistance genes, or the horizontal drug resistance genes transfer from other bacteria, resulting obtain drug resistance genes. Results In this study, 122 isolates of Vibrio parahaemolyticus were obtained for further pathogenicity identification, antibacterial susceptibility testing of 18 antimicrobial compounds and genetic characterization based on the whole genome sequencing. There is no pandemic serotype isolated between migratory birds, but 37 strains with cholera toxin. Five strains had col3M plasmid-moderately resistant drug-resistant strains of quinolone mediated by the qnrD1 gene. For the first time in China, Vibrio parahaemolyticus with col3M plasmid-mediated qnrD1 gene was isolated from migratory birds. Conclusion According to the mutltilocus sequence typing analysis, authors found the bacterial genetic diversity is higher, the clones are less and there is regional aggregation in Shenzhen. And mallards are more susceptible to Vibrio parahaemolyticus.

Emergence of a multidrug resistance efflux pump with carbapenem resistance gene blaVIM-2 in a Pseudomonas putida megaplasmid of migratory bird origin

2021 ◽  
Author(s):  
Ruichao Li ◽  
Kai Peng ◽  
Xia Xiao ◽  
Yuan Liu ◽  
Daxin Peng ◽  
...  
Keyword(s):  
Pseudomonas Putida ◽  
Resistance Genes ◽  
Bacterial Infections ◽  
Migratory Birds ◽  
Efflux Pump ◽  
Carbapenem Resistance ◽  
Migratory Bird ◽  
Vital Role ◽  
Pseudomonas Spp ◽  
Carbapenem Resistant

Abstract Background Tigecycline and carbapenems are regarded as vital antimicrobials to treat serious bacterial infections. Co-occurrence of resistance genes conferring resistance to both tigecycline and carbapenems in Pseudomonas spp. was not investigated. Objectives To characterize a megaplasmid co-harbouring tmexCD1-toprJ1 and blaVIM-2 in Pseudomonas putida of migratory bird origin. Methods One tigecycline- and carbapenem-resistant strain was isolated and characterized by antimicrobial susceptibility testing, conjugation assay, WGS and bioinformatics analysis. Results The strain P. putida ZXPA-20 resistant to meropenem and tigecycline was positive for blaVIM-2 and tmexCD1-toprJ1 genes. The gene blaVIM-2 was inserted into the backbone of the megaplasmid pZXPA-20 within a Tn5090-like structure. The genetic context of tmexCD1-toprJ1 in the megaplasmid was identical to many chromosomal tmexCD1-toprJ1 of Pseudomonas species. Plasmid-mediated tmexCD1-toprJ1 gene cluster in Pseudomonas spp. was more common than that in Klebsiella pneumoniae. To the best of our knowledge, this is the first report of co-occurrence of blaVIM-2 and tmexCD1-toprJ1 in one plasmid. Conclusions Emergence of plasmid-mediated carbapenem and tigecycline resistance genes in P. putida from migratory birds highlighted the importance of surveillance of novel mobile resistance genes in migratory birds, which may play a vital role in global transmission of novel resistance genes.

scholarly journals Development of a Set of Primers for Drug-Resistance Genes Detection in the Agents of Dangerous Bacterial Infections as Exemplified by Yersinia pestis, Vibrio cholerae, Escherichia coli Strains

2014 ◽  
pp. 57-60 ◽  
Author(s):  
K. A. Nikiforov ◽  
L. V. Anisimova ◽  
G. N. Odinokov ◽  
A. V. Fadeeva ◽  
L. A. Novichkova ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Drug Resistance ◽  
Yersinia Pestis ◽  
Vibrio Cholerae ◽  
Resistance Genes ◽  
Bacterial Infections ◽  
Pathogenic Bacteria ◽  
E Coli ◽  
Genes Encoding ◽  
Drug Resistant Strains

A set of primers for detection of genes encoding resistance to streptomycin ( strA, strB ), tetracyclin ( tetA, tetR ), chloramphenicol ( catА ), kanamycin ( npt , aphA ), vankomycin ( sanA ), polymyxin ( pmrD ) has been developed with the aim of rapid and effective detection of drug-resistant strains of dangerous bacterial infections agents. Efficacy of constructed primers has been confirmed against a panel of 40 Yersinia pestis, 49 Vibrio cholerae, and 2 Escherichia coli strains from the State collection of pathogenic bacteria of the RAPI “Microbe”. Drug-resistance genes ntp and catA have been detected in plague agent strains , strA, strB , npt , aphA , tetA and tetR - in cholera agent; strA , tetR , ntp and aphA - in pathogenic strain E. coli О157:H7. Determined is universal character of the designed primers for drug-resistance genes detection in these pathogenic bacteria species.

The gut microbiota resistome provides development of drug resistance in causative agents of human infectious diseases

2017 ◽  
pp. 20-32 ◽  
Author(s):  
Е.Н. Ильина ◽  
Е.И. Олехнович ◽  
А.В. Павленко
Keyword(s):  
Drug Resistance ◽  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Integrated Approach ◽  
Modern Medicine ◽  
Pathogenic Microorganisms ◽  
Human Pathogens ◽  
Potential Source ◽  
Causative Agents ◽  
Bacterial Genes

С течением времени подходы к изучению резистентности к антибиотикам трансформировались от сосредоточения на выделенных в виде чистой культуры патогенных микроорганизмах к исследованию резистентности на уровне микробных сообществ, составляющих биотопы человека и окружающей среды. По мере того, как продвигается изучение устойчивости к антибиотикам, возникает необходимость использования комплексного подхода для улучшения информирования мирового сообщества о наблюдаемых тенденциях в этой области. Все более очевидным становится то, что, хотя не все гены резистентности могут географически и филогенетически распространяться, угроза, которую они представляют, действительно серьезная и требует комплексных междисциплинарных исследований. В настоящее время резистентность к антибиотикам среди патогенов человека стала основной угрозой в современной медицине, и существует значительный интерес к определению ниши, в которых бактерии могут получить гены антибиотикорезистентности, и механизмов их передачи. В данном обзоре мы рассматриваем проблемы, возникшие на фоне широкого использования человечеством антибактериальных препаратов, в свете формирования микрофлорой кишечника резервуара генов резистентности. Over the time, studies of antibiotic resistance have transformed from focusing on pathogenic microorganisms isolated as a pure culture to analysis of resistance at the level of microbial communities that constitute human and environmental biotopes. Advancing studies of antibiotic resistance require an integrated approach to enhance availability of information about observed tendencies in this field to the global community. It becomes increasingly obvious that, even though not all resistance genes can geographically and phylogenetically spread, the threat they pose is indeed serious and requires complex interdisciplinary research. Currently, the antibiotic resistance of human pathogens has become a challenge to modern medicine, which is now focusing on determining a potential source for bacterial genes of drug resistance and mechanisms for the gene transmission. In this review, we discussed problems generated by the widespread use of antibacterial drugs in the light of forming a reservoir of resistance genes by gut microflora.

scholarly journals Culture-Independent Genotyping, Virulence and Antimicrobial Resistance Gene Identification of Staphylococcus aureus from Orthopaedic Implant-Associated Infections

2021 ◽  
Vol 9 (4) ◽  
pp. 707
Author(s):  
J. Christopher Noone ◽  
Fabienne Antunes Ferreira ◽  
Hege Vangstein Aamot
Keyword(s):  
Staphylococcus Aureus ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Virulence Gene ◽  
Orthopaedic Implant ◽  
Metagenomic Sequencing ◽  
Gene Detection ◽  
Shotgun Metagenomic Sequencing ◽  
Antimicrobial Resistance Genes ◽  
Culture Independent

Our culture-independent nanopore shotgun metagenomic sequencing protocol on biopsies has the potential for same-day diagnostics of orthopaedic implant-associated infections (OIAI). As OIAI are frequently caused by Staphylococcus aureus, we included S. aureus genotyping and virulence gene detection to exploit the protocol to its fullest. The aim was to evaluate S. aureus genotyping, virulence and antimicrobial resistance genes detection using the shotgun metagenomic sequencing protocol. This proof of concept study included six patients with S. aureus-associated OIAI at Akershus University Hospital, Norway. Five tissue biopsies from each patient were divided in two: (1) conventional microbiological diagnostics and genotyping, and whole genome sequencing (WGS) of S. aureus isolates; (2) shotgun metagenomic sequencing of DNA from the biopsies. Consensus sequences were analysed using spaTyper, MLST, VirulenceFinder, and ResFinder from the Center for Genomic Epidemiology (CGE). MLST was also compared using krocus. All spa-types, one CGE and four krocus MLST results matched Sanger sequencing results. Virulence gene detection matched between WGS and shotgun metagenomic sequencing. ResFinder results corresponded to resistance phenotype. S. aureus spa-typing, and identification of virulence and antimicrobial resistance genes are possible using our shotgun metagenomics protocol. MLST requires further optimization. The protocol has potential application to other species and infection types.

scholarly journals Draft Genome Sequence of the Shrimp Pathogen Vibrio parahaemolyticus ST17.P5-S1, Isolated in Peninsular Malaysia

2018 ◽  
Vol 7 (11) ◽  
Author(s):  
Sridevi Devadas ◽  
Subha Bhassu ◽  
Tze Chiew Christie Soo ◽  
Fatimah M. Yusoff ◽  
Mohamed Shariff
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Vibrio Parahaemolyticus ◽  
East Coast ◽  
Draft Genome ◽  
Antibiotic Resistance Genes ◽  
Peninsular Malaysia ◽  
Penaeus Vannamei ◽  
Content Type ◽  
Acute Hepatopancreatic Necrosis Disease

We sequenced the genome of Vibrio parahaemolyticus strain ST17.P5-S1, isolated from Penaeus vannamei cultured in the east coast of Peninsular Malaysia. The strain contains several antibiotic resistance genes and a plasmid encoding the Photorhabdus insect-related (Pir) toxin-like genes, pirAvp and pirBvp, associated with acute hepatopancreatic necrosis disease (AHPND).

scholarly journals Microevolution within ST11 group Clostridioides difficile isolates through mobile genetic elements based on complete genome sequencing

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yuan Wu ◽  
Lin Yang ◽  
Wen-Ge Li ◽  
Wen Zhu Zhang ◽  
Zheng Jie Liu ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Resistance Genes ◽  
Point Mutations ◽  
Evolutionary Process ◽  
Mobile Genetic Elements ◽  
Genetic Elements ◽  
Clostridioides Difficile ◽  
Hospitalized Elderly ◽  
Great Heterogeneity ◽  
High Level

Abstract Background Clade 5 Clostridioides difficile diverges significantly from the other clades and is therefore, attracting increasing attention due its great heterogeneity. In this study, we used third-generation sequencing techniques to sequence the complete whole genomes of three ST11 C. difficile isolates, RT078 and another two new ribotypes (RTs), obtained from three independent hospitalized elderly patients undergoing antibiotics treatment. Mobile genetic elements (MGEs), antibiotic-resistance, drug resistance genes, and virulent-related genes were analyzed and compared within these three isolates. Results Isolates 10,010 and 12,038 carried a distinct deletion in tcdA compared with isolate 21,062. Furthermore, all three isolates had identical deletions and point-mutations in tcdC, which was once thought to be a unique characteristic of RT078. Isolate 21,062 (RT078) had a unique plasmid, different numbers of transposons and genetic organization, and harboring special CRISPR spacers. All three isolates retained high-level sensitivity to 11 drugs and isolate 21,062 (RT078) carried distinct drug-resistance genes and loss of numerous flagellum-related genes. Conclusions We concluded that capillary electrophoresis based PCR-ribotyping is important for confirming RT078. Furthermore, RT078 isolates displayed specific MGEs, indicating an independent evolutionary process. In the further study, we could testify these findings with more RT078 isolates of divergent origins.

scholarly journals Molecular characteristics and virulence gene profiles of Staphylococcus aureus isolates in Hainan, China

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Xuehan Li ◽  
Tao Huang ◽  
Kai Xu ◽  
Chenglin Li ◽  
Yirong Li
Keyword(s):  
Staphylococcus Aureus ◽  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Virulence Genes ◽  
Mainland China ◽  
Geographical Location ◽  
Antibiotic Resistance Genes ◽  
Virulence Gene ◽  
Molecular Characteristics ◽  
Staphylococcal Protein A

Abstract Background There have been no reports regarding the molecular characteristics, virulence features, and antibiotic resistance profiles of Staphylococcus aureus (S. aureus) from Hainan, the southernmost province of China. Methods Two hundred twenty-seven S. aureus isolates, consisting of 76 methicillin-resistant S. aureus (MRSA) and 151 methicillin-susceptible S. aureus (MSSA), were collected in 2013–2014 and 2018–2019 in Hainan, and investigated for their molecular characteristics, virulence genes, antibiotic resistance profiles and main antibiotic resistance genes. Results Forty sequence types (STs) including three new STs (ST5489, ST5492 and ST5493), and 79 Staphylococcal protein A (spa) types were identified based on multilocus sequence typing (MLST) and spa typing, respectively. ST398 (14.1%, 32/227) was found to be the most prevalent, and the prevalence of ST398-MSSA increased significantly from 2013 to 2014 (5.5%, 5/91) to 2018–2019 (18.4%, 25/136). Seventy-six MRSA isolates were subject to staphylococcus chromosomal cassette mec (SCCmec) typing. SCCmec-IVa was the predominant SCCmec type, and specifically, ST45-SCCmec IVa, an infrequent type in mainland China, was predominant in S. aureus from Hainan. The antibiotic resistance profiles and antibiotic resistance genes of S. aureus show distinctive features in Hainan. The resistant rates of the MRSA isolates to a variety of antibiotics were significantly higher than those of the MSSA isolates. The predominant erythromycin and tetracycline resistance genes were ermC (90.1%, 100/111) and tetK (91.8%, 78/85), respectively. Eleven virulence genes, including the Panton-Valentine leukocidin (pvl) and eta, were determined, and the frequency of eta and pvl were found to be 57.3 and 47.6%. Such high prevalence has never been seen in mainland China before. Conclusion S. aureus isolates in Hainan have unique molecular characteristics, virulence gene and antibiotic resistance profiles, and main antibiotic resistance genes which may be associated with the special geographical location of Hainan and local trends in antibiotic use.

scholarly journals Using Bioacoustics to Examine Vocal Phenology of Neotropical Migratory Birds on a Wild and Scenic River in Arizona

Birds ◽  
2021 ◽  
Vol 2 (3) ◽  
pp. 261-274
Author(s):  
Heather L. Bateman ◽  
Sidney B. Riddle ◽  
Erin S. Cubley
Keyword(s):  
Sonoran Desert ◽  
Migratory Birds ◽  
Riparian Forest ◽  
Bird Species ◽  
Migratory Bird ◽  
Bird Diversity ◽  
Yellow Warbler ◽  
Habitat Features ◽  
The Usa ◽  
Vocal Activity

Passive acoustic recorders have been used successfully as automated survey tools to detect terrestrial wildlife. However, few studies have monitored Neotropical migratory bird use of riparian forest habitat using this technology. Within dryland ecosystems, the forests along rivers support high bird diversity. Many bird species of conservation concern require these floodplain forest habitats for foraging, migration stop-overs, and breeding. Few studies have explored the use of acoustic records in riverine systems designated for conservation for their natural resource value via the Wild and Scenic Rivers Act in the USA. Using acoustic recorders, we document vocal activity of four riparian-obligate species (Bell’s Vireo, Vireo bellii; Summer Tanager, Piranga rubra; Yellow Warbler, Setophaga petechial; and Yellow-billed Cuckoo, Coccyzus americanus) to determine species occurrence along a Wild and Scenic River. We established three study reaches along the perennial Lower Verde River, in the Sonoran Desert of central Arizona, USA. Nine acoustic recorders were used over the period of 80–120 days during the summer of 2018. We measured vegetation composition and structure in 100 m2 plots paired with acoustic recorders. Visualizing vocal activity showed that three species were calling and singing at each reach; whereas, one species, the cuckoo, had fewer recordings and occurred later in the summer. We demonstrate the utility of acoustic monitoring even when applied to rare birds in complex riparian habitats. This information is important for land management and conservation efforts concerning these species of interest and identifying important habitat features in Southwestern US riparian woodlands.

scholarly journals Hunting of migratory birds in North Sinai, Egypt

2015 ◽  
Vol 26 (1) ◽  
pp. 39-51 ◽  
Author(s):  
PERRI EASON ◽  
BASEM RABIA ◽  
OMAR ATTUM
Keyword(s):  
Migratory Birds ◽  
Bird Species ◽  
Migratory Bird ◽  
Mediterranean Coast ◽  
Population Declines ◽  
Mp3 Players ◽  
Southern Mediterranean ◽  
Sand Bar ◽  
North Sinai ◽  
Desert Scrub

SummaryDuring autumn migration, people set trammel nets along most of the Mediterranean coast of Egypt, with migrating Common Quail Coturnix coturnix as their primary target. These nets capture large numbers of quail, but also illegally capture other birds, which are then killed. We present the results of surveys from 2008 to 2012 along these lines of nets on the coast of North Sinai, Egypt. In desert scrub, which covers most of the Sinai coast, the mean number of quail killed reached a high of 357.1 per km per day in 2012, with a grand mean over the study period of 191.9 per km per day. Trammel nets also captured 54 other bird species in 28 families. Species captured at the highest rates in desert scrub included Corncrake Crex crex, Isabelline Wheatear Oenanthe isabellina and Greater Short-toed Lark Calandrella brachydactyla. Based on mean rates of capture from 2008 to 2012 in desert scrub and sand bar habitats, we estimate 2.0 million quail and 0.5 million birds of other species are killed annually in North Sinai during the 45 days of peak migration. In 2012, however, after the use of MP3 players to attract quail became widespread, we estimate that 3.3 million quail and 0.5 million other birds were captured. Hunters near the coast have recently begun covering shrubs and trees with mist nets to catch passerines. From 2010 to 2012, mist nets along our survey routes caught birds of 17 species in three families, with seven of these species caught only in this type of net. Hunting is likely to be a contributing factor to population declines for some species that migrate across Egypt and further studies of migratory bird hunting along the southern Mediterranean shore are badly needed.

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